Background The existing screening modalities for pulmonary embolism (PE), such as D-dimer and clinical prediction rules, have low positive predictive values. With its capability to indicate pulmonary vascular abnormalities, the ratio of the transfer factor of the lungs for nitric oxide and the transfer factor of the lungs for carbon monoxide (TL,NO/TL,CO) might be an additional discriminating parameter. Methods Carbon monoxide/Nitric oxide diffusion measurements were performed on unselected patients seen on the emergency department for which due to suspected PE a computed tomography pulmonary angiogram (CTPA) was ordered. Results A total of 28 patients were included, PE was found in 12 on CTPA. Median TL,NO/TL,CO ratio was 4·09 (interquartile range (IQR) 3·83–4·40) in the no PE group versus 4·00 (IQR 3·78–4·32) in the PE group (P = 0·959). Median alveolar volume was 77·1% of predicted in the no PE group versus 71·0% of predicted in the PE group (P = 0·353). Median TL,CO was 75·8% of predicted in the no PE group versus 68·8% of predicted in the PE group (P = 0·120). Median TL,NO was 69·3% of predicted in the no PE group versus 60·5% of predicted in the PE group (P = 0·078). Conclusion The presented data indicate that the TL,NO/TL,CO ratio cannot be used to exclude PE.